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MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000389266
MT speed 0 s - this script 2.88356 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GARS1disease_causing_automatic0.999999999999955simple_aaeaffected0G580Rsingle base exchangers137852646show file

Taster files

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999955 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM031187)
  • known disease mutation: rs9207 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:30668214G>CN/A show variant in all transcripts   IGV
HGNC symbol GARS1
Ensembl transcript ID ENST00000389266
Genbank transcript ID NM_002047
UniProt peptide P41250
alteration type single base exchange
alteration region CDS
DNA changes c.1738G>C
cDNA.1979G>C
g.33918G>C
AA changes G580R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 580
frameshift no
known variant Reference ID: rs137852646
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs9207 (pathogenic for Distal hereditary motor neuronopathy type 5|Distal spinal muscular atrophy) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM031187)

known disease mutation at this position, please check HGMD for details (HGMD ID CM031187)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031187)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3470.999
5.6911
(flanking)5.6911
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased33928wt: 0.27 / mu: 0.54wt: ACCTTCCTTCGGCCTGGGTAGGATCATGTATACGGTATTTG
mu: ACCTTCCTTCCGCCTGGGTAGGATCATGTATACGGTATTTG		 gtag|GATC
Acc increased33919wt: 0.33 / mu: 0.37wt: TGTAATTGAACCTTCCTTCGGCCTGGGTAGGATCATGTATA
mu: TGTAATTGAACCTTCCTTCCGCCTGGGTAGGATCATGTATA		 tcgg|CCTG
Acc marginally increased33918wt: 0.6961 / mu: 0.7497 (marginal change - not scored)wt: ATGTAATTGAACCTTCCTTCGGCCTGGGTAGGATCATGTAT
mu: ATGTAATTGAACCTTCCTTCCGCCTGGGTAGGATCATGTAT		 ttcg|GCCT
Acc increased33922wt: 0.67 / mu: 0.93wt: AATTGAACCTTCCTTCGGCCTGGGTAGGATCATGTATACGG
mu: AATTGAACCTTCCTTCCGCCTGGGTAGGATCATGTATACGG		 gcct|GGGT
Acc marginally increased33924wt: 0.9803 / mu: 0.9936 (marginal change - not scored)wt: TTGAACCTTCCTTCGGCCTGGGTAGGATCATGTATACGGTA
mu: TTGAACCTTCCTTCCGCCTGGGTAGGATCATGTATACGGTA		 ctgg|GTAG
Acc increased33923wt: 0.47 / mu: 0.90wt: ATTGAACCTTCCTTCGGCCTGGGTAGGATCATGTATACGGT
mu: ATTGAACCTTCCTTCCGCCTGGGTAGGATCATGTATACGGT		 cctg|GGTA
Donor increased33922wt: 0.55 / mu: 0.61wt: CGGCCTGGGTAGGAT
mu: CCGCCTGGGTAGGAT		 GCCT|gggt
Acc gained339200.90mu: GTAATTGAACCTTCCTTCCGCCTGGGTAGGATCATGTATAC ccgc|CTGG
Donor gained339230.31mu: CGCCTGGGTAGGATC CCTG|ggta
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      580EVVPNVIEPSFGLGRIMYTVFEHT
mutated  not conserved    580EVVPNVIEPSFRLGRIMYTVFEH
Ptroglodytes  all identical  ENSPTRG00000019042  580EVVPNVIEPSFGLGRIMYTVFEH
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000011415  506EVVPNVIEPSFGLGRIMYTVFEH
Mmusculus  all identical  ENSMUSG00000029777  570EVVPSVIEPSFGLGRIMYTILEH
Ggallus  all identical  ENSGALG00000005694  588EIVPNVIEPSFGIGRIMYTVFEH
Trubripes  all identical  ENSTRUG00000017557  611EVIPNVIEPSFGIGRIMYTIFEH
Drerio  all identical  ENSDARG00000059070  605EVVPNVIEPSFGIGRIMYSIFEH
Dmelanogaster  all identical  FBgn0027088  612EFIPSVVEPSFGIG
Celegans  all identical  T10F2.1  590EITPSVIEPSYGIGRIMYALLEH
Xtropicalis  all identical  ENSXETG00000018474  590EIVPNVIEPSFGLGRIMYTVF
protein features
start (aa)end (aa)featuredetails 
573580STRANDlost
576580REGIONSubstrate binding.lost
580583NP_BINDATP.lost
581592HELIXmight get lost (downstream of altered splice site)
593595STRANDmight get lost (downstream of altered splice site)
597600STRANDmight get lost (downstream of altered splice site)
603605STRANDmight get lost (downstream of altered splice site)
609611TURNmight get lost (downstream of altered splice site)
615621STRANDmight get lost (downstream of altered splice site)
625627TURNmight get lost (downstream of altered splice site)
628640HELIXmight get lost (downstream of altered splice site)
634634CONFLICTL -> S (in Ref. 3; BAG51964).might get lost (downstream of altered splice site)
635635MUTAGENS->L: Reduced activity.might get lost (downstream of altered splice site)
645647STRANDmight get lost (downstream of altered splice site)
654663HELIXmight get lost (downstream of altered splice site)
668672STRANDmight get lost (downstream of altered splice site)
674677HELIXmight get lost (downstream of altered splice site)
679681STRANDmight get lost (downstream of altered splice site)
683688STRANDmight get lost (downstream of altered splice site)
689691TURNmight get lost (downstream of altered splice site)
694698STRANDmight get lost (downstream of altered splice site)
699701TURNmight get lost (downstream of altered splice site)
702710HELIXmight get lost (downstream of altered splice site)
716722HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2220 / 2220
position (AA) of stopcodon in wt / mu AA sequence 740 / 740
position of stopcodon in wt / mu cDNA 2461 / 2461
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 242 / 242
chromosome 7
strand 1
last intron/exon boundary 2336
theoretical NMD boundary in CDS 2044
length of CDS 2220
coding sequence (CDS) position 1738
cDNA position
(for ins/del: last normal base / first normal base)		 1979
gDNA position
(for ins/del: last normal base / first normal base)		 33918
chromosomal position
(for ins/del: last normal base / first normal base)		 30668214
original gDNA sequence snippet ATGTAATTGAACCTTCCTTCGGCCTGGGTAGGATCATGTAT
altered gDNA sequence snippet ATGTAATTGAACCTTCCTTCCGCCTGGGTAGGATCATGTAT
original cDNA sequence snippet ATGTAATTGAACCTTCCTTCGGCCTGGGTAGGATCATGTAT
altered cDNA sequence snippet ATGTAATTGAACCTTCCTTCCGCCTGGGTAGGATCATGTAT
wildtype AA sequence MPSPRPVLLR GARAALLLLL PPRLLARPSL LLRRSLSAAS CPPISLPAAA SRSSMDGAGA
EEVLAPLRLA VRQQGDLVRK LKEDKAPQVD VDKAVAELKA RKRVLEAKEL ALQPKDDIVD
RAKMEDTLKR RFFYDQAFAI YGGVSGLYDF GPVGCALKNN IIQTWRQHFI QEEQILEIDC
TMLTPEPVLK TSGHVDKFAD FMVKDVKNGE CFRADHLLKA HLQKLMSDKK CSVEKKSEME
SVLAQLDNYG QQELADLFVN YNVKSPITGN DLSPPVSFNL MFKTFIGPGG NMPGYLRPET
AQGIFLNFKR LLEFNQGKLP FAAAQIGNSF RNEISPRSGL IRVREFTMAE IEHFVDPSEK
DHPKFQNVAD LHLYLYSAKA QVSGQSARKM RLGDAVEQGV INNTVLGYFI GRIYLYLTKV
GISPDKLRFR QHMENEMAHY ACDCWDAESK TSYGWIEIVG CADRSCYDLS CHARATKVPL
VAEKPLKEPK TVNVVQFEPS KGAIGKAYKK DAKLVMEYLA ICDECYITEM EMLLNEKGEF
TIETEGKTFQ LTKDMINVKR FQKTLYVEEV VPNVIEPSFG LGRIMYTVFE HTFHVREGDE
QRTFFSFPAV VAPFKCSVLP LSQNQEFMPF VKELSEALTR HGVSHKVDDS SGSIGRRYAR
TDEIGVAFGV TIDFDTVNKT PHTATLRDRD SMRQIRAEIS ELPSIVQDLA NGNITWADVE
ARYPLFEGQE TGKKETIEE*
mutated AA sequence MPSPRPVLLR GARAALLLLL PPRLLARPSL LLRRSLSAAS CPPISLPAAA SRSSMDGAGA
EEVLAPLRLA VRQQGDLVRK LKEDKAPQVD VDKAVAELKA RKRVLEAKEL ALQPKDDIVD
RAKMEDTLKR RFFYDQAFAI YGGVSGLYDF GPVGCALKNN IIQTWRQHFI QEEQILEIDC
TMLTPEPVLK TSGHVDKFAD FMVKDVKNGE CFRADHLLKA HLQKLMSDKK CSVEKKSEME
SVLAQLDNYG QQELADLFVN YNVKSPITGN DLSPPVSFNL MFKTFIGPGG NMPGYLRPET
AQGIFLNFKR LLEFNQGKLP FAAAQIGNSF RNEISPRSGL IRVREFTMAE IEHFVDPSEK
DHPKFQNVAD LHLYLYSAKA QVSGQSARKM RLGDAVEQGV INNTVLGYFI GRIYLYLTKV
GISPDKLRFR QHMENEMAHY ACDCWDAESK TSYGWIEIVG CADRSCYDLS CHARATKVPL
VAEKPLKEPK TVNVVQFEPS KGAIGKAYKK DAKLVMEYLA ICDECYITEM EMLLNEKGEF
TIETEGKTFQ LTKDMINVKR FQKTLYVEEV VPNVIEPSFR LGRIMYTVFE HTFHVREGDE
QRTFFSFPAV VAPFKCSVLP LSQNQEFMPF VKELSEALTR HGVSHKVDDS SGSIGRRYAR
TDEIGVAFGV TIDFDTVNKT PHTATLRDRD SMRQIRAEIS ELPSIVQDLA NGNITWADVE
ARYPLFEGQE TGKKETIEE*
speed 0.78 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
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Problems